Abdo is the author of No God But God: Egypt and the Triumph of Islam (2000), Mecca and Main Street: Muslim Life in America After 9/11, (2006), the monographThe New Sectarianism (Saban Center for Middle East Policy, 2013), and co-author of Answering Only to God: Faith and Freedom in Twenty-First Century Iran (2003). No God But God documents the social and political transformation of Egypt into an Islamic society and details leading figures and events responsible for giving moderate Islamists in Egypt enormous social and political power. Answering Only to God seeks to explain the theological struggle in Iran among the Shiite clerics and how it has led to political stagnation. Mecca and Main Street explores the changing identity among American Muslims as they struggle to keep true to their faith while deciding to what degree they will integrate into American society. The analysis paper The New Sectarianism, deals with Shia–Sunni relations post-Arab uprisings.[1][2][3]

Abdo has denounced the "secular Muslim agenda" she believes is promoted by some in America and Europe "because these ideas reflect a Western vision for the future of Islam." While many Westerners are ignorant of the Islamic revival, "in Britain, a growing number of Muslims advocate creating a court system based upon Islamic principles." [4] She has also warned that Islam is "separate but unequal" in American society, which has yet to "make room" for the "potent cultural and religious force" of Islam.[5] Abdo has strongly condemned the assassinations of nuclear scientists in Iran, and when asked about the claim of Iranian leadership that the bombs that damaged Israeli embassies February 13, 2012 had been planted by Israel itself, she replied that this was "entirely possible".[6]